Over on the X4U mailing list, cricket (an Apple mail.app engineer) wrote in with a process by which you can extract attachments from mail.app messages for storage in other locations. Here's what he wrote:

Navigate to ~/Library/Mail/Mailboxes in the Finder (or to the location where you have stored some mailboxes that you want to extract attachments from).

Find the mailbox you want to extract attachments from.

Control-click on the mailbox and choose 'Show Package Contents'.

Find the file called 'mbox' and option-drag it to another location (like the Desktop). Make sure to make a copy! Leave the original where it is.

Drag the 'mbox' file on Stuffit Expander.

Since Mail uses standard encoding formats for attachments, Stuffit will parse the file and save out every base64 encoded attachment and save it to disk.